I can currently only upload a sketch to my arduino BT when i press the reset-button before uploading.I would like to be able to remote-upload to the arduino AND I want to mount a motorshield on it, which makes the reset-button inaccessible to boot.

I was thinking I could desolder the reset-button of the BT, put in 2 transistors in its place, connect these to 2 digital pins from the BT.

I can then send a serial command, setting the pins to high, thus resetting the BT, then uploading the new sketch.

Would that work? Or is this a stupid idea and should I fix it in software?

No this is not recommended because as soon as the chip goes into reset it makes the pins tristate thus removing the reset before it has had chance to fully reset the processor. You need to trigger a one shot monostable to make that idea work.